Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1644
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58971
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:18053 original size:27 final size:27
Alignment explanation
Indices: 18015--18068 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
18005 TCTATAAAAC
18015 TTGTCATAAGCTCCTTTTTCGCAAGCT
1 TTGTCATAAGCTCCTTTTTCGCAAGCT
18042 TTGTCATAAGCTCCTTTTTCGCAAGCT
1 TTGTCATAAGCTCCTTTTTCGCAAGCT
18069 ACATATACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.41
Consensus pattern (27 bp):
TTGTCATAAGCTCCTTTTTCGCAAGCT
Found at i:18653 original size:4 final size:4
Alignment explanation
Indices: 18644--18671 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
18634 AAGTTTTATT
18644 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
18672 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:21073 original size:13 final size:12
Alignment explanation
Indices: 21042--21096 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
21032 ATGTAAACAG
*
21042 AAAAGAAATTGA
1 AAAAGAAGTTGA
21054 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
21066 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
21078 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
21090 AAAAGAA
1 AAAAGAA
21097 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:22466 original size:4 final size:4
Alignment explanation
Indices: 22457--22484 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
22447 AAGTTTTATT
22457 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
22485 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:24544 original size:18 final size:18
Alignment explanation
Indices: 24499--24551 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
24489 CATTTTCATA
* *
24499 CTCTTTCTTTTCTTTACT
1 CTCTTTATTTTCTTTTCT
*
24517 CATC-TCATTTTCTTTTCT
1 C-TCTTTATTTTCTTTTCT
24535 CTCTTTATTTTTCTTTT
1 CTCTTTA-TTTTCTTTT
24552 TTTTACAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 2 0.07
18 15 0.54
19 11 0.39
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.68
Consensus pattern (18 bp):
CTCTTTATTTTCTTTTCT
Found at i:39822 original size:21 final size:23
Alignment explanation
Indices: 39777--39823 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39767 TCACCTGCAA
* *
39777 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
39800 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39821 TAA
1 TAA
39824 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:41171 original size:333 final size:331
Alignment explanation
Indices: 40567--41211 Score: 1146
Period size: 333 Copynumber: 1.9 Consensus size: 331
40557 ATTGCTCGCG
** * *
40567 GACCAAGATCGAGTTGCCAAGTCACGAAAAACTCCTACGAAAACCCTAAACAATCAGATTCGAAA
1 GACCAAGATCGAGTCACCAAGTCACGAAAAACTCCTACGAAAACCCTAAACAATCAGATCCAAAA
*
40632 CGAAACAGAAAATTAATAGATTAGAACTTTGAATTTCCAGATCTGAAATAAAATCCCCAAATCAG
66 CGAAACAGAAAATTAAAAGATTAGAACTTTGAATTTCCAGATCTGAAATAAAATCCCCAAATCAG
*
40697 CAAAGAATCAAATTGAGAATAGAAATAAGTGTTGGGTTCTTGAAACCCTCAAGGAGATTGTGATT
131 CAAAGAATCAAATTCAGAATAGAAATAAGTGTTGGGTTCTTGAAACCCTCAAGGAGATTGTGATT
*
40762 CTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTTGACAATCTAATTTCACCCAAAAAGAG
196 CTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAATCTAATTTCACCCAAAAAGAG
* * *
40827 TATGGAAAAACCCTAGAAATTGGGGATTTTTGGGCTGATTCCTTAAGATAGATGATAGAGGAATG
261 CATGGAAAAACCCTAAAAATTGGGAATTTTTGGGCTGATTCCTTAAGATAGATGATAGAGGAATG
40892 CGCGCA
326 CGCGCA
* ** *
40898 GACCAAGATCGAGTCATCAAGTCACGGGAAACTTCTACGAAAACCCTAAACAATCAGATCCAAAA
1 GACCAAGATCGAGTCACCAAGTCACGAAAAACTCCTACGAAAACCCTAAACAATCAGATCCAAAA
40963 CGAAACAGAAAAATTAAAAGATTAGAACTTTGAATTTCCAGATCTGAAATAAAATCCCCAAATCA
66 CGAAACAG-AAAATTAAAAGATTAGAACTTTGAATTTCCAGATCTGAAATAAAATCCCCAAATCA
41028 GCAAAGAATCAAATTCAGAATAGAAATAAGTGTTAGGGTTCTTGAAACCCTCAAGGAGATTGTGA
130 GCAAAGAATCAAATTCAGAATAGAAATAAGTGTT-GGGTTCTTGAAACCCTCAAGGAGATTGTGA
41093 TTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAATCTAATTTCACCCAAAAAG
194 TTCTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAATCTAATTTCACCCAAAAAG
41158 AGCATGGAAAAACCCTAAAAATTGGGAATTTTTGGGCTGATTCCTTAAGATAGA
259 AGCATGGAAAAACCCTAAAAATTGGGAATTTTTGGGCTGATTCCTTAAGATAGA
41212 AAAAGGCTGA
Statistics
Matches: 298, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
331 65 0.22
332 88 0.30
333 145 0.49
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (331 bp):
GACCAAGATCGAGTCACCAAGTCACGAAAAACTCCTACGAAAACCCTAAACAATCAGATCCAAAA
CGAAACAGAAAATTAAAAGATTAGAACTTTGAATTTCCAGATCTGAAATAAAATCCCCAAATCAG
CAAAGAATCAAATTCAGAATAGAAATAAGTGTTGGGTTCTTGAAACCCTCAAGGAGATTGTGATT
CTGCCCAATTGAACACCAAGATAGTTTTCCCCAAATTTCGACAATCTAATTTCACCCAAAAAGAG
CATGGAAAAACCCTAAAAATTGGGAATTTTTGGGCTGATTCCTTAAGATAGATGATAGAGGAATG
CGCGCA
Found at i:46632 original size:16 final size:16
Alignment explanation
Indices: 46611--46644 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
46601 TTACCTCGCT
46611 TACCTTCAGGCTCATG
1 TACCTTCAGGCTCATG
46627 TACCTTCAGGCTCATG
1 TACCTTCAGGCTCATG
46643 TA
1 TA
46645 GTGTGATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (16 bp):
TACCTTCAGGCTCATG
Found at i:49659 original size:14 final size:16
Alignment explanation
Indices: 49640--49671 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
49630 CGACAAGCTT
49640 TATCAA-AA-ATGGGC
1 TATCAATAATATGGGC
49654 TATCAATAATATGGGC
1 TATCAATAATATGGGC
49670 TA
1 TA
49672 AATCAAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (16 bp):
TATCAATAATATGGGC
Found at i:55195 original size:1 final size:1
Alignment explanation
Indices: 55189--55221 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
55179 AAGCTTTATG
55189 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
55222 AAAACGTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.